RetrogeneDB ID: retro_cjac_1040

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:55241564..55242701(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012871
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBMS1
• Ensembl ID: ENSCJAG00000014861
• Aliases: None
• Description: RNA binding motif, single stranded interacting protein 1 [Source:HGNC Symbol;Acc:9907]

Sequence

>retro_cjac_1040
AAGCAGACTCCGGTCCCAGCCCACCCCATGGCCCCTCCCAGTCCCAGCACCACCTGCAGTAATAACAACAGTAGCAGCAG
TAGCAACTCAGGATGGGATCAGATCAGCGAAATGAACCTCTATATCCGAGGACTGCCTCCCCACACCACCGACCAGGACC
TGGTGAAGCTCTGTCAACCATATGGGAAAATAGTCTCCACAAAGGCAATATTGGATAAGACAACGAACAAATGCAAAGGT
TACGGTTTTGTGGACTTTGACAGCCCTGCCGCAGCTCAAAAAGCTGTGTCTGCCCTGAAGGCCAGTGGGGTTCAAGCTCA
AATGGCAAAGCAACAGGAACAAGATCCTACGAACCTGTGCATTTCTAATTTGCCACTCTCCATGGATGAGCAAGAACTGG
AAAATATGCTCAAACCATTTGGACAGGTTATTTCTACAAGGATACTGCGTGATTCCAGTGGTACAAGTCGTGGTGTTGGC
TTTGCTAGGATGGAATCAACAGAAAAATGCGAAGCTGTTATTGGTCATTTTAATGGAAAATTTATTAAGACACCACCAGG
AGTTTCTGCCCCCACAGAACCTTTATTGTGTAAGTTCGCGGATGGAGGACAGAAAAAGAGACAGAACCCAAACAAATACA
TCCCTAATGGAAGACCATGGCATAGAGAAGGAGAGGCTGGAATGACACTTGCTTACGACCCAACTACAGCCGCCCTACAG
AACGGATTTTATCCTTCACCATACAGTATTGCTACAAACCGAATGATCACTCAAACTTCTATTACACCCTATATTGCATC
TCCTGTATCTGCCTACCAGGTGCAAAGTCCTTCTTGGATGCAACCCCAGCCATATATTCTACAACACCCCGGTGCCGTGC
TAACTCCCTCAATGGAGCACACCATGTCACTACAGCCCGCATTCATGATCAGCCCTCTGGTCCAGCGGATGAGTCATCTG
TCGCTAGGCAGCACTGGAACATACATGCCTGCAAGGTCAGCTATGCAAGGAGCCTACTTGCCACAGTATGCACATATGCA
GACGACAGCGGTTCCTGTTGAGGAGGCAAGTGGTCAACAGCAGGTGGCTGTCGAAACGTCTAATGACCGTTCTCCGTATA
CCTTTCAACCCAATAAG

Alignment

ORF - retro_cjac_1040 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.81 %
• Parental protein coverage: 94.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQSLVPAHPMAPPSPSTTSSNNNSSSSSNSGWDQLSKTNLYIRGLPPHTTDQDLVKLCQPYGKIVSTKAI
          KQ..VPAHPMAPPSPSTT.SNNNSSSSSNSGWDQ.S..NLYIRGLPPHTTDQDLVKLCQPYGKIVSTKAI
Retrocopy KQTPVPAHPMAPPSPSTTCSNNNSSSSSNSGWDQISEMNLYIRGLPPHTTDQDLVKLCQPYGKIVSTKAI

Parental  LDKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPF
          LDKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNL.ISNLPLSMDEQELENMLKPF
Retrocopy LDKTTNKCKGYGFVDFDSPAAAQKAVSALKASGVQAQMAKQQEQDPTNLCISNLPLSMDEQELENMLKPF

Parental  GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFADGGQKKRQNP
          GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFADGGQKKRQNP
Retrocopy GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFADGGQKKRQNP

Parental  NKYIPNGRPWHREGEVRLAGMTLTYDPTTAALQNGFYPSPYSIATNRMITQTSITPYIASPVSAYQVQSP
          NKYIPNGRPWHREGE...AGMTL.YDPTTAALQNGFYPSPYSIATNRMITQTSITPYIASPVSAYQVQSP
Retrocopy NKYIPNGRPWHREGE---AGMTLAYDPTTAALQNGFYPSPYSIATNRMITQTSITPYIASPVSAYQVQSP

Parental  SWMQPQPYILQHPGAVLTPSMEHTMSLQPASMISPLAQQMSHLSLGSTGTYMPATSAMQGAYLPQYAHMQ
          SWMQPQPYILQHPGAVLTPSMEHTMSLQPA.MISPL.Q.MSHLSLGSTGTYMPA.SAMQGAYLPQYAHMQ
Retrocopy SWMQPQPYILQHPGAVLTPSMEHTMSLQPAFMISPLVQRMSHLSLGSTGTYMPARSAMQGAYLPQYAHMQ

Parental  TTAVPVEEASGQQQVAVETSNDHSPYTFQPNK
          TTAVPVEEASGQQQVAVETSND.SPYTFQPNK
Retrocopy TTAVPVEEASGQQQVAVETSNDRSPYTFQPNK

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	0.07 RPM	15.49 RPM
SRP051959_heart	0.28 RPM	33.71 RPM
SRP051959_kidney	0.07 RPM	27.00 RPM
SRP051959_liver	0.04 RPM	14.56 RPM
SRP051959_lung	0.20 RPM	42.69 RPM
SRP051959_lymph_node	0.14 RPM	22.76 RPM
SRP051959_skeletal_muscle	0.11 RPM	15.37 RPM
SRP051959_spleen	0.19 RPM	45.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1040 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Callithrix jacchus	ENSCJAG00000014861	1 retrocopy	retro_cjac_1040 ,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000153250	1 retrocopy	retro_hsap_1131,