RetrogeneDB ID: retro_acar_176

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343316.1:954666..955782(-)
• Located in intron of: ENSACAG00000017076

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSACAG00000015238
• Aliases: None
• Description: None

Sequence

>retro_acar_176
ATGGATAATGATATCGCTGCGCTCGTGGTTGACAACGTCTCCGGAATATGCAAGGCTGGCTTTGCCGGCGATGATGCCCC
TCGCGCCGTGTTCCCGTCCATCGTCGGCCACCTCAGGCACCAGGGCGTGATGGGCCAGAAAGACAGCTACGTTGGGGATG
AGGTGCAGAATAAAAGAGACATCCTGACCCTGAAGTATCCCATTGAACACTGCATCGTCACCAACTGGGACAACATGGAA
AAGATCTGGCACCACACTTTCTACAACAAGTTGAGAGTCGCCCCCGAAGAACACCCCATGCTGCTGACAGAGGCCCCCTT
GAACCCCAAAGCCAACAGAGAAAAGATGACACAGATCATGTTTGAGACCTTCAACACCCCCGCCATGTACGTGGCCATCC
AGGCTGTGCTGTCCCTGTACGCCTCTGGCTGCACCACCGGCATTGTGATGGACTCTGGCGACGGCATCACCCACACTGTG
CCCATCTATGCAGGTTATGCCCTGCCCCACGCCATCCTCTGCTTGGACCTGGCCGGCCGCGACTTAACAGACTACCTCAT
GAAGATCTTGACCGAGAGAGGCTACAGCTTCACCACCACGGCCAAGAGGGAAATTGTCCGCGACATCAAGGAGAAGCTCT
GCTACGTCGCGCTCGACTTCGAGCAGGAGATGGCTACCGTGGCTTCCAGCTCATCCTTGGAAAAGAGCTACGAACTCCCC
GACAGGCAGGTGATCACCATCGGCAACAAGCGGTTCAGGTGCCCAGAGGCCCTCTTCCAGCCATCCTTTTTGGGTATGGA
GTCCTGTGGCATTCAAGAAACCACCTTCAACTCCATCATGCAGTGCGACGTGGATATCCGCAAAGATCTGTACGCCAACA
CCGTCCTGTCTGGCGGCAACACCATGTACCCCGGTATCGCCGACAGGATGTAGAAGGAGATCACAGCCCTGGCTCCCAGC
ACAATGAAAATCAAGATCATTGCCCCGCCGGAGTGTAAATACTCCGTCTGGATCGGAGGCTCCATCTTTACCTCCCTGTC
GACCTTCCAGCAGATGTGAGTCAGCAAGCAAGAGTACGACGAATCCGGACCTTCCATCGTCCACCGCAAATGCTTC

Alignment

ORF - retro_acar_176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          M...IAALV.DN.SG.CKAGFAGDDAPRAVFPSIVG..RHQGV...MGQKDSYVGDE.Q.KR.ILTLKYP
Retrocopy MDNDIAALVVDNVSGICKAGFAGDDAPRAVFPSIVGHLRHQGV---MGQKDSYVGDEVQNKRDILTLKYP

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
          IEH.IVTNWD.MEKIWHHTFYN.LRVAPEEHP.LLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
Retrocopy IEHCIVTNWDNMEKIWHHTFYNKLRVAPEEHPMLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL

Parental  SLYASG-TTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          SLYASG.TTGIVMDSGDG.THTVPIY.GYALPHAIL.LDLAGRDLTDYLMKILTERGYSFTTTA.REIVR
Retrocopy SLYASGCTTGIVMDSGDGITHTVPIYAGYALPHAILCLDLAGRDLTDYLMKILTERGYSFTTTAKREIVR

Parental  DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
          DIKEKLCYVALDFEQEMAT.ASSSSLEKSYELPD.QVITIGN.RFRCPEALFQPSFLGMESCGI.ETTFN
Retrocopy DIKEKLCYVALDFEQEMATVASSSSLEKSYELPDRQVITIGNKRFRCPEALFQPSFLGMESCGIQETTFN

Parental  SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SIM.CDVDIRKDLYANTVLSGG.TMYPGIADRM.KEITALAPSTMKIKIIAPPE.KYSVWIGGSI..SLS
Retrocopy SIMQCDVDIRKDLYANTVLSGGNTMYPGIADRM*KEITALAPSTMKIKIIAPPECKYSVWIGGSIFTSLS

Parental  TFQQMWISKQEYDESGPSIVHRKCF
          TFQQM..SKQEYDESGPSIVHRKCF
Retrocopy TFQQM*VSKQEYDESGPSIVHRKCF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP009831_adrenal	13.82 RPM	2616.14 RPM
SRP009831_brain	3.69 RPM	1706.37 RPM
SRP009831_dewlap	2.74 RPM	2044.29 RPM
SRP009831_embryo	30.56 RPM	3431.76 RPM
SRP009831_heart	4.77 RPM	891.39 RPM
SRP009831_liver	15.91 RPM	1343.35 RPM
SRP009831_lung	34.25 RPM	1634.50 RPM
SRP009831_ovary	3.63 RPM	1631.70 RPM
SRP009831_skeletal_muscle	1.27 RPM	188.12 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_176 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_176 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 143 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176 , retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Bos taurus	ENSBTAG00000006189	2 retrocopies	retro_btau_286, retro_btau_903,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macropus eugenii	ENSMEUG00000016247	57 retrocopies	retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Microcebus murinus	ENSMICG00000014863	3 retrocopies	retro_mmur_23, retro_mmur_352, retro_mmur_6,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
Otolemur garnettii	ENSOGAG00000008040	3 retrocopies	retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,