RetrogeneDB ID: retro_pabe_1737

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:620544..621739(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTBP2
• Ensembl ID: ENSPPYG00000002746
• Aliases: None
• Description: C-terminal binding protein 2 [Source:HGNC Symbol;Acc:2495]

Sequence

>retro_pabe_1737
ATGGCCCTTGTGGATAAGCGCTAAGTCAAGAGACAGCGACTGGACAGAATTGTGAAGGAATTCGCCGCCAGATCATGAAA
GACCCCCTAAGCCCCCAATCACTGGCGGCATTGCTGGTCGGCCATGACTGCACTGTGGACATGCCCATGCGGAAGGACCT
GGCCACCGTGGCCTTCTGTGATGCAGTCCACGCAGGAGATCGACGAGAAAGTTCCAAACGGAGCCGTGGGGGCCATGATG
TACCACACCATCACCTCAACAGGGAGGATCTGGCAAATTTCAAGGCTTTGAGAGTGATCGTGCAGGTTGGCAGTGGCTAT
GACAACGTGTACATCAAGGCTGCAGGTGAGCTCGGAATTGCTACGTGAAACATCCCGTCCGCAGCCGTGGAAGAGACAGC
CGACTCCACCATCTGCCACATCCTCAACATGTACCGGAGGAACACACGGCTGTAACAGGCACTGTGGGAAGGCAAGCGAG
TCCAACGCGTGGAGCAGACCTGCGAGGTGGCCTCGGGAGTGGCCCGCGTTCGTGGGTAGACGCTGGGCCTCATCGGCTAC
AGTCGCACGCAGCAGGCTTTTGCAGTTCCAGCCACTGCCTTTGGATTCAGCGTCATATTTTATTACCCCTACTTGCAGGA
TGGGATCGAGCAGTCCCTGGGCGTGCAGAGGGTCTACACACAGCAGGAATTGCTGTATCAGAGAGACTGCGTCTCCTTGC
ACTACAGTCTCAGCGAACATAAACACCACCTCATCAATGACTTTACCAGAAAGCAGATGAGGCAGGGAGCATTCATTGTG
AACACAGCCCGTGGTGGCCTGGAGGATGAGAAAGCCTTAGCACATGTCCTCAAGGAGGGCAGGATACGAGGGGCAGTCCT
CGACCTGAATGAGTCGTAGCCCTTTAGCTTTGCTCAGGTCCGTTGAAAGATGCCCCCAGTCTCATCTGCACTCCTCACAC
TGCCTGCTACAGCGAGCAGGTGTCACTGGAGATGAGGGAGACAGCTGCCACCGAGATCCGCCGAGCCATCACAGGTCGCA
TCCCAGGAACCTTAAGAAACTGTGTCAACAAGGAATTCTTTGTCACATTTGTGCTTTGGTGGGAAATAGACCAGCAAGCA
ATTCATCCAGTCATCGTGGGCGTGGCTCCAGGAGGACTTCCTGCAGCCATGGAAGGGATCTTCCCTGGAGACATC

Alignment

ORF - retro_pabe_1737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 89.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALVDKHKVKRQRLDRI-CEGIRPQIMNGPLHPRPLVALLDGRDCTVEMPILKDLATVAFCDAQSTQEIH
          MALVDK..VKRQRLDRI.CEGIR.QIM..PL.P..L.ALL.G.DCTV.MP..KDLATVAFCDA.......
Retrocopy MALVDKR*VKRQRLDRI<CEGIRRQIMKDPLSPQSLAALLVGHDCTVDMPMRKDLATVAFCDAVHAGDRR

Parental  EKVLNEAVGAMMYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTI
          E.......G....H...L.REDL..FKALRVIV..GSGYDNV.IKAAGELGIA..NIPSAAVEETADSTI
Retrocopy ESSKRSRGGHDVPHH-HLNREDLANFKALRVIVQVGSGYDNVYIKAAGELGIAT*NIPSAAVEETADSTI

Parental  CHILNLYRRNTWLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFY
          CHILN.YRRNT.L.QAL.EG.RVQ.VEQ..EVASG.AR.RG.TLGLIG..RT.QA.AV.A.AFGFSVIFY
Retrocopy CHILNMYRRNTRL*QALWEGKRVQRVEQTCEVASGVARVRG*TLGLIGYSRTQQAFAVPATAFGFSVIFY

Parental  DPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEK
          .PYLQDGIE.SLGVQRVYT.Q.LLYQ.DCVSLH..L.EH.HHLINDFT.KQMRQGAF.VN.ARGGL.DEK
Retrocopy YPYLQDGIEQSLGVQRVYTQQELLYQRDCVSLHYSLSEHKHHLINDFTRKQMRQGAFIVNTARGGLEDEK

Parental  ALAQALKEGRIRGAALDVHESEPFSFAQ-GPLKDAPNLICTPHTAWYSEQASLEMREAAATEIRRAITGR
          ALA..LKEGRIRGA.LD..ES.PFSFAQ.GPLKDAP.LICTPHTA.YSEQ.SLEMRE.AATEIRRAITGR
Retrocopy ALAHVLKEGRIRGAVLDLNES*PFSFAQ<GPLKDAPSLICTPHTACYSEQVSLEMRETAATEIRRAITGR

Parental  IPESLRNCVNKEFFVTSAPWSVIDQQAIHPELNG-ATYRYPPGIVGVAPGGL
          IP..LRNCVNKEFFVT...W..IDQQAIHP...G.A....P....G..PG..
Retrocopy IPGTLRNCVNKEFFVTFVLWWEIDQQAIHPVIVGVAPGGLPAAMEGIFPGDI

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.96 RPM
SRP007412_cerebellum	0.00 RPM	15.81 RPM
SRP007412_heart	0.00 RPM	3.97 RPM
SRP007412_kidney	0.00 RPM	15.51 RPM
SRP007412_liver	0.00 RPM	2.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1737 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1737 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012775	1 retrocopy	retro_cfam_1868,
Callithrix jacchus	ENSCJAG00000012539	2 retrocopies	retro_cjac_1866, retro_cjac_2528,
Homo sapiens	ENSG00000175029	1 retrocopy	retro_hsap_403,
Oryctolagus cuniculus	ENSOCUG00000007076	1 retrocopy	retro_ocun_378,
Pongo abelii	ENSPPYG00000002746	10 retrocopies	retro_pabe_1706, retro_pabe_1710, retro_pabe_1711, retro_pabe_1719, retro_pabe_1737 , retro_pabe_1750, retro_pabe_1773, retro_pabe_3228, retro_pabe_3230, retro_pabe_3587,