RetrogeneDB ID: retro_tbel_422

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2029:267988..268675(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000010102
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSTBEG00000010781
• Aliases: None
• Description: actin, gamma 1 [Source:HGNC Symbol;Acc:144]

Sequence

>retro_tbel_422
CTGCTGACAGAGGGCCCCCCTGAGCCCCAAAGCCAATGGAAAGTAGATGACCCAGCTCATGTTTGAGACCTTCAACACCC
CAGTCAGGTACATGGCCGTCCAGATGGGGCTGTCCCTATTTGACTCTGATCCCACCACCGGTATTGTCATGGACTCAGAC
AACAGGGTCACCCACATGGTGCCTATCTATGAGGGCTAAGCCCTCCTGCATGCCATCCTGTGTCTGGACCTGGCTGACCT
GGACCTGAGGGACTACCTCATGAAGATCCTTACTGAGCATAGCTACAGCTTCATCACCATGGCAGAACGAGAAATTCTGT
ACAACATCGAGAAGAAGTTGTGCTACATTGCCCTGGACTTTGAGTAGGAAACAGCAGCGGTCGCATCCTCCTCCTCCCTG
GAAAAGAGCTTCTAGCTGACTGATGGCCAGGTCATCACCATCTGCAACAAACACTTCCAGTGTCTATAGGCGCTGTTCCA
GTGGTCCTTCTTGGGCATGGAGTCCTGCGGCAGCCAGGAGACCACCTTCAATTTCATCATGAAGTGTGATGTGGACATGT
CCAAGGACCTATATGCCAACGCAGTGCTGTCCACAACACTGCCATGTACCCAGGCATCGCCAACCAGATGCAGAAGGAGA
TCACAGCTCTGGCACCCAGCACCATAAAGATAAAGATCATTGCCCCA

Alignment

ORF - retro_tbel_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 84.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLTE-APLNPKNREK-MTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALP
          LLTE.APL.PK...K.MTQ.MFETFNTP..Y.A.Q..LSL..S..TTGIVMDS...VTH.VPIYEG.AL.
Retrocopy LLTE>APLSPKANGK*MTQLMFETFNTPVRYMAVQMGLSLFDSDPTTGIVMDSDNRVTHMVPIYEG*ALL

Parental  HAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL
          HAIL.LDLA..DL.DYLMKILTE..YSF.T.AEREI...I..KLCY.ALDFE.E.A..ASSSSLEKS..L
Retrocopy HAILCLDLADLDLRDYLMKILTEHSYSFITMAEREILYNIEKKLCYIALDFE*ETAAVASSSSLEKSF*L

Parental  PDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS-GGTTMYPGIAD
          .DGQVITI.N..F.C..ALFQ.SFLGMESCG..ETTFN.IMKCDVD..KDLYAN.VLS...T.MYPGIA.
Retrocopy TDGQVITICNKHFQCL*ALFQWSFLGMESCGSQETTFNFIMKCDVDMSKDLYANAVLS<HNTAMYPGIAN

Parental  RMQKEITALAPSTMKIKIIAP
          .MQKEITALAPST.KIKIIAP
Retrocopy QMQKEITALAPSTIKIKIIAP

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_422 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_422 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 16 parental genes, and 87 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
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,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sorex araneus	ENSSARG00000012197	1 retrocopy	retro_sara_267,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Tupaia belangeri	ENSTBEG00000010781	1 retrocopy	retro_tbel_422 ,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,