RetrogeneDB ID: retro_cjac_2538

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:80759305..80761321(+)
• Located in intron of: ENSCJAG00000037104

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP72
• Ensembl ID: ENSCJAG00000017998
• Aliases: None
• Description: signal recognition particle 72kDa [Source:HGNC Symbol;Acc:11303]

Sequence

>retro_cjac_2538
ATGGCGAGCGGCGGCAGCGGGGGGCGGGTTTCAGTGCCTGCGCTGTGGAGTGAAGTGAACCGGTATGGCCAGAACGGCGA
CTTCACGCGCGCTCTCAAGACCGTCAATAAGATACTACAGAGCAACAAAGATGATGTAACTGCCCTGCATTGTAAAGTGG
TATGCCTTATCCAGAATGGAAGTTTCAAGGAAGCCTTGAATGTCATCAATACTCACACCAAAGTGTTAGCCAATAACTCT
CTCTCCTTTGAAAAGGCATATTGCGAGTACAGGCTAAACAGAATTGAGAATGCCTTGAAGACGATAGAAAATTCCACCCA
GCAGACAGACAAACTGAAGGAGCTTTATGGACAAGTGTTATACCGTTTGGAATGCTATGATGAATGCTTAGCGGTATATA
GAGATCTTGTCCGAAACTCCCAAGATGATTATGATGAGGAGAGGAAAACAAACCTTTCAGCAGTTGTTGCAGCTCAGAGC
AATTGGGAAAAAGTGGTTCCGGAGAACTTGGGCTTCCAGGAAGGCACACACGAGCTGTGCTACAACACTGCATGTGCACT
GATAGGCCAAGGCCAGCTGAACCAAGCCATGAAAATCCTGCAAAAAGCTGAAGATCTTTGCCGCCGTTCATTATCAGAAG
ATGCTGATGGTACTGAGGAGGACCCACAGGCAGAACTGGCCATCATTCATGGTCAGATGGCCTATATTCTGCAGCTTCAG
GGTCGAACAGAGGAGGCTTTGCAACTTTACAATCAAATAATAAAACTAAAACCAACAGATGTGGGATTACTAGCTGTAAT
TGCAAATAACATCATTACCATTAACAAGGACCAAAATGTCTTTGAATCCAAGAAGAAAGTGAAATTAACCAATGCGGAAG
GAGTAGAGTTTAAGCTTTCCAAGAAACAGCTACAAGCTATAGAGTTTAACAAAGCTTTACTTGCTATGTATACAAACCAG
GCAGAACAATGCCGCAGAATATCTGCCAGTTTACAGTCCCAAAGCCCTGAGCATCTCTTACCTGTGTTAATCCAAGCTGC
CCAGCTCTACGGTGAAAAGCAGCACACAAAAGCAGTTGAGCTGCTTCAGGAATTTTCAGATCAGCATCCAGAAAATGCAG
CTGAAATTAAGCTGACCATGGCACAGTTGAAAATTTCTCAAGGTAATATTTCTAAAGCATGTCTAATATTGAGAAGCATA
CAGGAGTTAAATCATAAACCAGGCGTGGTGTCTGCATTAGTGACCATGTATCGTCATGAAGAAGATATTGATAGTGCCAT
TGAGGTCTTCACACAAGCTATCCAGTGGTATCAAAGCCATCAGCCCAAATCTGCTGCTCATTTGTCCTTGATAAGAGAAG
CTGCAAACTTCAAACTCAAATATGGGCGGAAGAAGGAGGCAATTAGTGACCTAGAACAGCTATGGAAACAAAATCCAAAA
GATATTCACACCCTTGCACAGCTTATTTCTGCTTACCCGCTTGTAGATCCAGAGAAAGCCAAAGCTCTTAGTAAACACTT
GCCATCGTCAGATAGTATGTCTCTCAAAGTAGATGTTGAGGCTCTTGAAAATTCTCCTGGTGCTACATATATTCGGAAAA
AGGGTGGAAAAGTTACTGGAGATAGTCAACCAAAGGAACAAGGACAGGGAGATTTGAAAAAGAAGAAAAAGAAAAAGAAG
GGAAAATTGCCTAAGAATTACGACCCAAAAGTTACCCCAGATCCAGAAAGATGGCTGCCAATGCGAGAACGTTCTTACTA
CCGGGGAAGAAAGAAGGGTAAAAAGAAGGATCAGATTGGAAAAGGGACCCAGGGAGCAACTACAGGAGCTTCATCTGAAC
TGGATGCCAGTAAAACTGTGAGCAGCCCACCCACCTCCCCAAGACCTGGCAGTGCAGCAACAGTATCTGCCTCTACAAGT
AACATCATACCCCCAAGACACCAGAAACCTGCAGGGGCTCCAGCAACAAAAAAGAAACAGCAACAGAAAAAGAAGAAAGG
TGGAAAAGGTGGCTGG

Alignment

ORF - retro_cjac_2538 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGGSGG-VSVPALWSEVNRYGQNGDFTRALKTVNKILQSNKDDVTALHCKVVCLIQNGSFKEALNVIN
          MASGGSGG.VSVPALWSEVNRYGQNGDFTRALKTVNKILQSNKDDVTALHCKVVCLIQNGSFKEALNVIN
Retrocopy MASGGSGGRVSVPALWSEVNRYGQNGDFTRALKTVNKILQSNKDDVTALHCKVVCLIQNGSFKEALNVIN

Parental  THTKVLANNSLSFEKAYCEYRLNRIENALKTIENSTQQTDKLKELYGQVLYRLERYDECLVVYRDLVRNS
          THTKVLANNSLSFEKAYCEYRLNRIENALKTIENSTQQTDKLKELYGQVLYRLE.YDECL.VYRDLVRNS
Retrocopy THTKVLANNSLSFEKAYCEYRLNRIENALKTIENSTQQTDKLKELYGQVLYRLECYDECLAVYRDLVRNS

Parental  QDDYDEERKTNLSAVVAAQSNWEKVVPENLGFQEGTHELCYNTACALIGQGQLNQAMKILQKAEVDLCRR
          QDDYDEERKTNLSAVVAAQSNWEKVVPENLGFQEGTHELCYNTACALIGQGQLNQAMKILQKAE.DLCRR
Retrocopy QDDYDEERKTNLSAVVAAQSNWEKVVPENLGFQEGTHELCYNTACALIGQGQLNQAMKILQKAE-DLCRR

Parental  SLSEDADGTEEDPQAELAIIHGQMAYILQLQGRTEEALQLYNQIIKLKPTDVGLLAVIANNIITINKDQN
          SLSEDADGTEEDPQAELAIIHGQMAYILQLQGRTEEALQLYNQIIKLKPTDVGLLAVIANNIITINKDQN
Retrocopy SLSEDADGTEEDPQAELAIIHGQMAYILQLQGRTEEALQLYNQIIKLKPTDVGLLAVIANNIITINKDQN

Parental  VFDSKKKVKLTNAEGVEFKLSKKQLQAIEFNKALLAMYTNQAEQCRRISASLQSQSPEHLLPVLIQAAQL
          VF.SKKKVKLTNAEGVEFKLSKKQLQAIEFNKALLAMYTNQAEQCRRISASLQSQSPEHLLPVLIQAAQL
Retrocopy VFESKKKVKLTNAEGVEFKLSKKQLQAIEFNKALLAMYTNQAEQCRRISASLQSQSPEHLLPVLIQAAQL

Parental  CREKQHTKAIELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIQELNHKPGMVSALVTMYSH
          ..EKQHTKA.ELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIQELNHKPG.VSALVTMY.H
Retrocopy YGEKQHTKAVELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIQELNHKPGVVSALVTMYRH

Parental  EEDIDSAIEVFTQAIQWYQSHQPKSAAHLSLIREAANFKLKYGRKKEAISDLEQLWKQNPKDIHTLAQLI
          EEDIDSAIEVFTQAIQWYQSHQPKSAAHLSLIREAANFKLKYGRKKEAISDLEQLWKQNPKDIHTLAQLI
Retrocopy EEDIDSAIEVFTQAIQWYQSHQPKSAAHLSLIREAANFKLKYGRKKEAISDLEQLWKQNPKDIHTLAQLI

Parental  SAYSLVDPEKAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVTGDSQPKEQGQGDLKKKKKKK
          SAY.LVDPEKAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVTGDSQPKEQGQGDLKKKKKKK
Retrocopy SAYPLVDPEKAKALSKHLPSSDSMSLKVDVEALENSPGATYIRKKGGKVTGDSQPKEQGQGDLKKKKKKK

Parental  KGKLPKNYDPKVTPDPERWLPMRERSYYRGRKKGKKKDQIGKGTQGATTGASSELDASKTVSSPPTSPRP
          KGKLPKNYDPKVTPDPERWLPMRERSYYRGRKKGKKKDQIGKGTQGATTGASSELDASKTVSSPPTSPRP
Retrocopy KGKLPKNYDPKVTPDPERWLPMRERSYYRGRKKGKKKDQIGKGTQGATTGASSELDASKTVSSPPTSPRP

Parental  GSAATVSASTSNIIPPRHQKPAGAPATKKKQQQKKKKGGKGGW
          GSAATVSASTSNIIPPRHQKPAGAPATKKKQQQKKKKGGKGGW
Retrocopy GSAATVSASTSNIIPPRHQKPAGAPATKKKQQQKKKKGGKGGW

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	2.68 RPM	25.23 RPM
SRP051959_heart	1.79 RPM	15.05 RPM
SRP051959_kidney	2.55 RPM	21.32 RPM
SRP051959_liver	4.46 RPM	37.28 RPM
SRP051959_lung	3.07 RPM	22.87 RPM
SRP051959_lymph_node	2.69 RPM	24.73 RPM
SRP051959_skeletal_muscle	2.84 RPM	20.11 RPM
SRP051959_spleen	3.30 RPM	28.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2538 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2538 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017998	1 retrocopy	retro_cjac_2538 ,
Homo sapiens	ENSG00000174780	2 retrocopies	retro_hsap_1939, retro_hsap_3685,
Nomascus leucogenys	ENSNLEG00000008806	1 retrocopy	retro_nleu_2909,
Oryctolagus cuniculus	ENSOCUG00000012226	1 retrocopy	retro_ocun_989,
Rattus norvegicus	ENSRNOG00000002100	1 retrocopy	retro_rnor_587,