RetrogeneDB ID: retro_cjac_2589

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:9289105..9290113(-)
• Located in intron of: ENSCJAG00000021148

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSCJAG00000015197
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_cjac_2589
CTCTTCCGCTGCCATTTTAAATCCGGCTCCATGCAACGCTCCGCCGCTGCTGCCGCCGCGACCCGGACTGTGCGCCAGCA
CCTCCCTGCCGACAGCTTCGCCGCTATGGAGGACATGAACAAGTACGGCAACATAGAGGAATTTGCAGAGGGATCCAAGA
TCAACGCGAGCAAGAATCAGCGGGATGACAGTAAAATGTTTATTGGAGGCTTGAGCTGGGATACAAGCAAAAAAGATCTG
ACTGAATATTTGTCTCGATTTGGGGAAGTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGGGAGATCAAGAGGATT
TGGATTTGTGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTGGATGGCAAATTGA
TAGATCCCAAAAGGGCCAAAGCTTTAAAAGGGAAAGAACCTCCCAAAAAGGTTTTTGTGGGTGGATTAAGCCCGGATACT
TCTGAAGAACAAATTAAAGAATATTTTGGAGCCTTTGGAGAGACTGAAAACATTGAACTTCCCATGGATACAAAAACAAA
TGAGAGAAGAGGATATTGTTTTATCACATATACCGACGAAGAGCCAGTAAAAAAATTGTTAGAAAGCAGATACCATCAGA
TTGGTTCTGGGAAGTGTGAAATAAAACTTGCACAACCCAAAGAGGTATATAGGCAGCAACAGCAACAACAAAAAGGTGGA
AGAGGTGCTGCAGCTGGTGTACGAGGTGGTACGAGGGGTCGTGGCCGAGGTCAGGGCCAAAACTGGAACCAAGGATTTAA
TAACTATTATGATCAAGGATATGAAAATTACAATAGTGCCTATGGTGGTGATCAAAACTATAGTGGCTATGGCGGATATG
ATTATACTGGGTATAACTATGGGAACTATGGATATGGACAGGGATATGCAGACTACAGTGGCCAACAGAGCACTTATGGC
AAGGCATCTTGAGGGGGTGGCAATCACCAAAATAATTACCAGCCATAC

Alignment

ORF - retro_cjac_2589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.54 %
• Parental protein coverage: 80.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFRRHFKSGSIQRSAAAAAATRTARQHPPADSSAAMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
          LFR.HFKSGS.QRSAAAAAATRT.RQH.PADS.AAMEDMN.Y.NIEEFAEGSKINASKNQ.DD.KMFIGG
Retrocopy LFRCHFKSGSMQRSAAAAAATRTVRQHLPADSFAAMEDMNKYGNIEEFAEGSKINASKNQRDDSKMFIGG

Parental  LSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
          LSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK
Retrocopy LSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAK

Parental  ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESR
          ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGE.ENIELPMDTKTNERRG.CFITYTDEEPVKKLLESR
Retrocopy ALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGETENIELPMDTKTNERRGYCFITYTDEEPVKKLLESR

Parental  YHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNSA
          YHQIGSGKCEIK.AQPKEVYRQQQQQQKGGRGAAAG.RGGTRGRGRGQGQNWNQGFNNYYDQGY.NYNSA
Retrocopy YHQIGSGKCEIKLAQPKEVYRQQQQQQKGGRGAAAGVRGGTRGRGRGQGQNWNQGFNNYYDQGYENYNSA

Parental  YGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
          YGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKAS.GGGNHQNNYQPY
Retrocopy YGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKAS*GGGNHQNNYQPY

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	0.33 RPM	43.44 RPM
SRP051959_heart	0.35 RPM	73.46 RPM
SRP051959_kidney	0.82 RPM	92.78 RPM
SRP051959_liver	0.54 RPM	58.46 RPM
SRP051959_lung	0.37 RPM	92.27 RPM
SRP051959_lymph_node	0.14 RPM	110.34 RPM
SRP051959_skeletal_muscle	0.37 RPM	67.81 RPM
SRP051959_spleen	0.25 RPM	110.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2589 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2589 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2589 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007908	2 retrocopies	retro_cjac_2285, retro_cjac_3041,
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589 ,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,