RetrogeneDB ID: retro_cjac_2972

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:38256229..38256950(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000017416
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLIC1
• Ensembl ID: ENSCJAG00000002788
• Aliases: None
• Description: chloride intracellular channel 1 [Source:HGNC Symbol;Acc:2062]

Sequence

>retro_cjac_2972
ATGGCTGAAAAACAACCGCCGGTCGAATTGTTTGTGAAGGCTGGCAGTGATGGGGCCAAGATTGGGAACTGCCCCTTCTC
CCAGAGACTGTTCATGGTCCTGTGGCTCAGGGAGTCACCTTCAACGTTACCACAGTTGACACCAAGAGGCAGACCGAGAC
AGTGCAAAGCTGTGCCCAGGAGGGCAGCTCCCATTCCTGCTGTATGGCACTGAAGTGCACACAGACACCAACAAGATTGA
GGAATTTCTGGAGGCAGTGCTATGCCCTCCCAGGTACCCCAAGCTGGCAGCTCTGAACCCTGAGTCCAACACAGCTGGGC
TGGACATATTTGCCAAATTTTCTGCCTACATCAAGAATTCAAACCCAGCACTCAATGATAATCTGGAGAAGGGACTCCTG
AAAGCCCTGAAGGTTTTAGACAATTACTTAACATCCCCCCTCCCAGAAGAAGTGGATGAAACCAGTGCTGAAGATGAGGG
CATCTCTCAGAGGAAGTTTCTGGATGGCAATGAGCTCACCCTGGCTGACTGCAACCTGTTGCCAAAGCTACACATAGTAC
AGGTGGTATGTAAGAAATACAGGGGATTCACTATCCCTGAGGCCTTCTGGGGAGTGCATCGGTACTTGAGCAATGCCTAC
GCAAGGGAAGAATTCGCCTTCACCTGTCCAGATGATGAGGAAATTGAGCTCGCCTATGAGCAAGTGGCCAAGGCCCTCAA
A

Alignment

ORF - retro_cjac_2972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEEQPPVELFVKAGSDGAKIGNCPFSQRLFMVLWLK-GVTFNVTTVDTKRRTETVQ-KLCPGGQLPFLL
          MAE.QPPVELFVKAGSDGAKIGNCPFSQRLFMVLWL..GVTFNVTTVDTKR.TETVQ.KLCPGGQLPFLL
Retrocopy MAEKQPPVELFVKAGSDGAKIGNCPFSQRLFMVLWLR<GVTFNVTTVDTKRQTETVQ<KLCPGGQLPFLL

Parental  YGTEVHTDTNKIEEFLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPALNDNLEKGLLKALK
          YGTEVHTDTNKIEEFLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPALNDNLEKGLLKALK
Retrocopy YGTEVHTDTNKIEEFLEAVLCPPRYPKLAALNPESNTAGLDIFAKFSAYIKNSNPALNDNLEKGLLKALK

Parental  VLDNYLTSPLPEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFTIPEAFRGVHR
          VLDNYLTSPLPEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFTIPEAF.GVHR
Retrocopy VLDNYLTSPLPEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFTIPEAFWGVHR

Parental  YLSNAYAREEFASTCPDDEEIELAYEQVAKALK
          YLSNAYAREEFA.TCPDDEEIELAYEQVAKALK
Retrocopy YLSNAYAREEFAFTCPDDEEIELAYEQVAKALK

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	0.09 RPM	88.77 RPM
SRP051959_heart	0.07 RPM	22.50 RPM
SRP051959_kidney	0.04 RPM	34.63 RPM
SRP051959_liver	0.00 RPM	11.16 RPM
SRP051959_lung	0.07 RPM	48.10 RPM
SRP051959_lymph_node	0.05 RPM	42.40 RPM
SRP051959_skeletal_muscle	0.02 RPM	8.63 RPM
SRP051959_spleen	0.00 RPM	40.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2972 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000621	2 retrocopies	retro_cfam_481, retro_cfam_525,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972 ,
Callithrix jacchus	ENSCJAG00000020833	2 retrocopies	retro_cjac_1713, retro_cjac_461,
Dipodomys ordii	ENSDORG00000016424	3 retrocopies	retro_dord_506, retro_dord_524, retro_dord_550,
Felis catus	ENSFCAG00000019049	1 retrocopy	retro_fcat_1301,
Gorilla gorilla	ENSGGOG00000011331	1 retrocopy	retro_ggor_2153,
Macropus eugenii	ENSMEUG00000015201	1 retrocopy	retro_meug_254,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166,
Nomascus leucogenys	ENSNLEG00000006264	3 retrocopies	retro_nleu_1296, retro_nleu_24, retro_nleu_2894,
Oryctolagus cuniculus	ENSOCUG00000022545	1 retrocopy	retro_ocun_1449,
Otolemur garnettii	ENSOGAG00000031840	4 retrocopies	retro_ogar_2402, retro_ogar_3273, retro_ogar_407, retro_ogar_982,
Procavia capensis	ENSPCAG00000013268	1 retrocopy	retro_pcap_30,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238, retro_ptro_724,
Sarcophilus harrisii	ENSSHAG00000006493	1 retrocopy	retro_shar_28,
Tarsius syrichta	ENSTSYG00000001540	2 retrocopies	retro_tsyr_1452, retro_tsyr_722,