RetrogeneDB ID: retro_cjac_2997

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:86037670..86038846(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021564
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BNIP2
• Ensembl ID: ENSCJAG00000014722
• Aliases: None
• Description: BCL2/adenovirus E1B 19kDa interacting protein 2 [Source:HGNC Symbol;Acc:1083]

Sequence

>retro_cjac_2997
GCTTCCGGGTCAGCTGCTGCCACCGTCGCTGTGCCGCTGCGGCCGGGGGATTGGGCCGGGGACTCCACCGCCGACCGAGG
GGAGCGGGCTCCGCTCGGCGCCGCTTTTTGCGACCTGGCCGTCAGCCCCACGTCGCCGGCCTGGAGGGGCGAGGAGGACG
AGGGGGCCAAGGCTTCCTCCGGGGACATTGGCCCTCTGGATTATCAAGAGTTTGTAGCTGACATTGAATCCAGGCTGAGG
ATAGAAGGTGTGGAACTTAAAGAAGAATGGCAAGATGAAGATTTTCCAATACCTTTACCAGAAGATGATAGTACTGAAGC
AGATATACTGGCTATAACTGGACCAGAGAACCGGCCTGGTTCCCTAGAAGTCAATGAAAATAAAGTGAGAAAGAAACTAA
TGCCTCCAGACATTAGCCTGACACTGGATCCTAGCGATGGCTCTGTGTTGTCGGACGATCTGGATGAAAGTGGGGAGATT
GAGTTAGATGGCTTAGACACACCCTCTGAGAATGAGTTTGAGTGGGAAGATGATCTTCCAAAACCCAAGACTACTGAAGT
AATTAGGAAAGGCTCAATTACTGAATATACAGCAGCAGAGGAAAAAGAAGATGGACGACGCTGGCGTATGTTCAGGATTG
GAGAGCAGGACCACAGAGTTGACATGAAAGCGATTGAACCCTATAAAAAAGTTATCAGCCATGGGGGATATTATGGGGAT
GGATTAAATGCCATTGTTGTGTTTGCTGTCTGTTTCATGCCTGAAAGTAGTCAACCTAACTATAGATACGTGATGGACAA
TCTCTTTAAATATGTTATTGGCACTTTGGAGCTATTGGTAGCAGAGAACTACATGATAGTTTATTTAAATGGTGCGACAA
CTCGAAGAAAAATGCCCAGTCTGGGGTGGCTCAGGAAATGTTATCAGCAAATCGATAGAAGGTTACGGAAAAATCTAAAA
TCCCTAATCATTGTACATCCTTCTTGGTTTATCAGAACACTTCTGGCTGTTACAAGACCATTTATTAGCTCAAAATTCAG
TCAAAAAATTAGATACGTCTTTAATTTGGCAGAACTAGCAGAACTTGTCCCCATGGAATACGTTGGCATACCAGAATGCA
TAAAACAAGTTGATCAAGAGCTTAATGGAAAGCAAGACGAACCGAGAAATGAACAG

Alignment

ORF - retro_cjac_2997 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.97 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASGSAAAVAAVPLRPGDWAGVSTADRGERAPLGAAFCDLAVSPTSPAWRGEEDEGAKASSGDIGPLDYQE
          ASGSAAA..AVPLRPGDWAG.STADRGERAPLGAAFCDLAVSPTSPAWRGEEDEGAKASSGDIGPLDYQE
Retrocopy ASGSAAATVAVPLRPGDWAGDSTADRGERAPLGAAFCDLAVSPTSPAWRGEEDEGAKASSGDIGPLDYQE

Parental  FVADIESRLRMEGVELKEEWQDEDFPIPLPEDDSTEADILAITGPENQPGSLEVNENKVRKKLMPPDISL
          FVADIESRLR.EGVELKEEWQDEDFPIPLPEDDSTEADILAITGPEN.PGSLEVNENKVRKKLMPPDISL
Retrocopy FVADIESRLRIEGVELKEEWQDEDFPIPLPEDDSTEADILAITGPENRPGSLEVNENKVRKKLMPPDISL

Parental  TLDPSDGSVLSDDLDESGEIELDGLDTPSENSNEFEWEDDLPKPKTTEVIRKGSITEYTAAEEKEDGRRW
          TLDPSDGSVLSDDLDESGEIELDGLDTPSEN..EFEWEDDLPKPKTTEVIRKGSITEYTAAEEKEDGRRW
Retrocopy TLDPSDGSVLSDDLDESGEIELDGLDTPSEN--EFEWEDDLPKPKTTEVIRKGSITEYTAAEEKEDGRRW

Parental  RMFRIGEQDHRVDMKAIEPYKKVISHGGYYGDGLNAIVVFAVCFMPESSQPNYRYLMDNLFKYVIGTLEL
          RMFRIGEQDHRVDMKAIEPYKKVISHGGYYGDGLNAIVVFAVCFMPESSQPNYRY.MDNLFKYVIGTLEL
Retrocopy RMFRIGEQDHRVDMKAIEPYKKVISHGGYYGDGLNAIVVFAVCFMPESSQPNYRYVMDNLFKYVIGTLEL

Parental  LVAENYMIVYLNGATTRRKMPSLGWLRKCYQQIDRRLRKNLKSLIIVHPSWFIRTLLAVTRPFISSKFSQ
          LVAENYMIVYLNGATTRRKMPSLGWLRKCYQQIDRRLRKNLKSLIIVHPSWFIRTLLAVTRPFISSKFSQ
Retrocopy LVAENYMIVYLNGATTRRKMPSLGWLRKCYQQIDRRLRKNLKSLIIVHPSWFIRTLLAVTRPFISSKFSQ

Parental  KIRYVFNLAELAELVPMEYVGIPECIKQVDQELNGKQDEPRNEQ
          KIRYVFNLAELAELVPMEYVGIPECIKQVDQELNGKQDEPRNEQ
Retrocopy KIRYVFNLAELAELVPMEYVGIPECIKQVDQELNGKQDEPRNEQ

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
SRP051959_colon	0.24 RPM	26.67 RPM
SRP051959_heart	0.46 RPM	56.16 RPM
SRP051959_kidney	0.13 RPM	24.80 RPM
SRP051959_liver	0.32 RPM	21.68 RPM
SRP051959_lung	0.39 RPM	56.29 RPM
SRP051959_lymph_node	0.21 RPM	44.43 RPM
SRP051959_skeletal_muscle	0.37 RPM	44.20 RPM
SRP051959_spleen	0.42 RPM	57.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2997 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2997 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014722	1 retrocopy	retro_cjac_2997 ,
Cavia porcellus	ENSCPOG00000004962	2 retrocopies	retro_cpor_393, retro_cpor_935,