RetrogeneDB ID: retro_amel_929

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192753.1:344776..345469(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSAMEG00000016015
• Aliases: None
• Description: actin, gamma 1 [Source:HGNC Symbol;Acc:144]

Sequence

>retro_amel_929
TATGCTTCTGGCCACACCACTGGTATTGTCATGGACTCTGAGGATGAGGTAACCCACACTGTACCCATTTACGAGGGGCA
CACCTTGCCCCATGCCATCCTGTGTCTGGACTGGTTGGACAGGTCATACCTCCTCAAGATCCTCATGGAGGGTGGTTACA
GCTTCACCACCACCGCCGAGTGGGAAATCGTGCATGACATCAAGGAGAAGCTCTGCTACATCGCTCTGGATTTCAAGCAG
GAGATGGCCATCATCTCATCCTCCTCCTCCCTGGAGAAGAGCTACGAGCTGCCGGGTGGGCAGGTGATCACCAGTGGCAA
CGAGGGGTTCCCCTGTCCCAAGGTGCTCTTCCAGCCTTCCTTCCTGGGTATGGAGTCCTGTGGCATCCATGAGACCACCT
TCAACTCCATCATGAAGTGTGACATCGACATCCAGAAGGACCACTACACTAACACGGTGCTGTCTGGTGGGTCCACCATG
TACTCCAGCATCGCAGACAAGATGCAGATGCAGAAGACCACAGCGCTGGCACCCAGCATGATGAAGATCAAGATCACCTC
TCCTCTGGAACACAAATACTCCGCGTCGATCGGGGGCTCCATCCTGGCCTCACGTTCCACCTTCCAGCAGATATGGATCA
GCAAGCAGGAGTATGATGAGTTGGGCCCCTCCACCGTCCACCACATATGCTTC

Alignment

ORF - retro_amel_929 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 62.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDI
          YASG.TTGIVMDS.D.VTHTVPIYEG..LPHAIL.LD...R....YL.KIL.E.GYSFTTTAE.EIV.DI
Retrocopy YASGHTTGIVMDSEDEVTHTVPIYEGHTLPHAILCLDWLDRS---YLLKILMEGGYSFTTTAEWEIVHDI

Parental  KEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSI
          KEKLCY.ALDF.QEMA...SSSSLEKSYELP.GQVIT.GNE.F.CP..LFQPSFLGMESCGIHETTFNSI
Retrocopy KEKLCYIALDFKQEMAIISSSSSLEKSYELPGGQVITSGNEGFPCPKVLFQPSFLGMESCGIHETTFNSI

Parental  MKCDVDIRKDLYANTVLSGGTTMYPGIADRMQ-KEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
          MKCD.DI.KD.Y.NTVLSGG.TMY..IAD.MQ....TALAPS.MKIKI..P.E.KYS..IGGSILAS.ST
Retrocopy MKCDIDIQKDHYTNTVLSGGSTMYSSIADKMQMQKTTALAPSMMKIKITSPLEHKYSASIGGSILASRST

Parental  FQQMWISKQEYDESGPSIVHRKCF
          FQQ.WISKQEYDE.GPS.VH..CF
Retrocopy FQQIWISKQEYDELGPSTVHHICF

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_929 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_929 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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.

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929 ,
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,
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	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
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,
Sorex araneus	ENSSARG00000012197	1 retrocopy	retro_sara_267,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Tupaia belangeri	ENSTBEG00000010781	1 retrocopy	retro_tbel_422,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,